-
1
-
-
79952674000
-
Interactome networks and human disease
-
1 Vidal, M., et al. Interactome networks and human disease. Cell 144 (2011), 986–998.
-
(2011)
Cell
, vol.144
, pp. 986-998
-
-
Vidal, M.1
-
2
-
-
84959344911
-
The ORFeome Collaboration: a genome-scale human ORF-clone resource
-
2 The ORFeome Collaboration, The ORFeome Collaboration: a genome-scale human ORF-clone resource. Nat. methods 13 (2016), 191–192.
-
(2016)
Nat. methods
, vol.13
, pp. 191-192
-
-
The ORFeome Collaboration1
-
3
-
-
84948067587
-
A human interactome in three quantitative dimensions organized by stoichiometries and abundances
-
3 Hein, M.Y., et al. A human interactome in three quantitative dimensions organized by stoichiometries and abundances. Cell 163 (2015), 712–723.
-
(2015)
Cell
, vol.163
, pp. 712-723
-
-
Hein, M.Y.1
-
4
-
-
84937213168
-
The BioPlex network: a systematic exploration of the human interactome
-
4 Huttlin, E.L., et al. The BioPlex network: a systematic exploration of the human interactome. Cell 162 (2015), 425–440.
-
(2015)
Cell
, vol.162
, pp. 425-440
-
-
Huttlin, E.L.1
-
5
-
-
84911474471
-
A proteome-scale map of the human interactome network
-
5 Rolland, T., et al. A proteome-scale map of the human interactome network. Cell 159 (2014), 1212–1226.
-
(2014)
Cell
, vol.159
, pp. 1212-1226
-
-
Rolland, T.1
-
6
-
-
84942031770
-
Panorama of ancient metazoan macromolecular complexes
-
6 Wan, C., et al. Panorama of ancient metazoan macromolecular complexes. Nature 525 (2015), 339–344.
-
(2015)
Nature
, vol.525
, pp. 339-344
-
-
Wan, C.1
-
7
-
-
77956040602
-
High-quality binary interactome mapping
-
7 Dreze, M., et al. High-quality binary interactome mapping. Methods in enzymol. 470 (2010), 281–315.
-
(2010)
Methods in enzymol.
, vol.470
, pp. 281-315
-
-
Dreze, M.1
-
8
-
-
84925224926
-
The yeast two-hybrid assay: still finding connections after 25 years
-
8 Vidal, M., Fields, S., The yeast two-hybrid assay: still finding connections after 25 years. Nat. methods 11 (2014), 1203–1206.
-
(2014)
Nat. methods
, vol.11
, pp. 1203-1206
-
-
Vidal, M.1
Fields, S.2
-
9
-
-
82355163586
-
Benchmarking a luciferase complementation assay for detecting protein complexes
-
9 Cassonnet, P., et al. Benchmarking a luciferase complementation assay for detecting protein complexes. Nat. methods 8 (2011), 990–992.
-
(2011)
Nat. methods
, vol.8
, pp. 990-992
-
-
Cassonnet, P.1
-
10
-
-
18144394763
-
Capturing protein interactions in the secretory pathway of living cells
-
10 Nyfeler, B., et al. Capturing protein interactions in the secretory pathway of living cells. Proc. Natl. Acad. Sci. U.S.A. 102 (2005), 6350–6355.
-
(2005)
Proc. Natl. Acad. Sci. U.S.A.
, vol.102
, pp. 6350-6355
-
-
Nyfeler, B.1
-
11
-
-
0035199166
-
Design and application of a cytokine-receptor-based interaction trap
-
11 Eyckerman, S., et al. Design and application of a cytokine-receptor-based interaction trap. Nat. cell biol. 3 (2001), 1114–1119.
-
(2001)
Nat. cell biol.
, vol.3
, pp. 1114-1119
-
-
Eyckerman, S.1
-
12
-
-
84949233942
-
High-resolution CRISPR screens reveal fitness genes and genotype-specific cancer liabilities
-
12 Hart, T., et al. High-resolution CRISPR screens reveal fitness genes and genotype-specific cancer liabilities. Cell 163 (2015), 1515–1526.
-
(2015)
Cell
, vol.163
, pp. 1515-1526
-
-
Hart, T.1
-
13
-
-
53349117774
-
High-quality binary protein interaction map of the yeast interactome network
-
13 Yu, H., et al. High-quality binary protein interaction map of the yeast interactome network. Science 322 (2008), 104–110.
-
(2008)
Science
, vol.322
, pp. 104-110
-
-
Yu, H.1
-
14
-
-
0034628487
-
Guilt-by-association goes global
-
14 Oliver, S., Guilt-by-association goes global. Nature 403 (2000), 601–603.
-
(2000)
Nature
, vol.403
, pp. 601-603
-
-
Oliver, S.1
-
15
-
-
0034628508
-
A comprehensive analysis of protein–protein interactions in Saccharomyces cerevisiae
-
15 Uetz, P., et al. A comprehensive analysis of protein–protein interactions in Saccharomyces cerevisiae. Nature 403 (2000), 623–627.
-
(2000)
Nature
, vol.403
, pp. 623-627
-
-
Uetz, P.1
-
16
-
-
84954289195
-
A proteome-wide fission yeast interactome reveals network evolution principles from yeasts to human
-
16 Vo, T.V., et al. A proteome-wide fission yeast interactome reveals network evolution principles from yeasts to human. Cell 164 (2016), 310–323.
-
(2016)
Cell
, vol.164
, pp. 310-323
-
-
Vo, T.V.1
-
17
-
-
84865677098
-
A census of human soluble protein complexes
-
17 Havugimana, P.C., et al. A census of human soluble protein complexes. Cell 150 (2012), 1068–1081.
-
(2012)
Cell
, vol.150
, pp. 1068-1081
-
-
Havugimana, P.C.1
-
18
-
-
0037161731
-
Comparative assessment of large-scale data sets of protein–protein interactions
-
18 von Mering, C., et al. Comparative assessment of large-scale data sets of protein–protein interactions. Nature 417 (2002), 399–403.
-
(2002)
Nature
, vol.417
, pp. 399-403
-
-
von Mering, C.1
-
19
-
-
84961226693
-
Characterizing protein–protein interactions using mass spectrometry: challenges and opportunities
-
19 Smits, A.H., Vermeulen, M., Characterizing protein–protein interactions using mass spectrometry: challenges and opportunities. Trends in biotechnol. 34 (2016), 834–835.
-
(2016)
Trends in biotechnol.
, vol.34
, pp. 834-835
-
-
Smits, A.H.1
Vermeulen, M.2
-
20
-
-
67649634849
-
Defining the human deubiquitinating enzyme interaction landscape
-
20 Sowa, M.E., et al. Defining the human deubiquitinating enzyme interaction landscape. Cell 138 (2009), 389–403.
-
(2009)
Cell
, vol.138
, pp. 389-403
-
-
Sowa, M.E.1
-
21
-
-
58149305794
-
An empirical framework for binary interactome mapping
-
21 Venkatesan, K., et al. An empirical framework for binary interactome mapping. Nat. methods 6 (2009), 83–90.
-
(2009)
Nat. methods
, vol.6
, pp. 83-90
-
-
Venkatesan, K.1
-
22
-
-
7444252784
-
Human ORFeome version 1.1: a platform for reverse proteomics
-
22 Rual, J.F., et al. Human ORFeome version 1.1: a platform for reverse proteomics. Genome Res. 14 (2004), 2128–2135.
-
(2004)
Genome Res.
, vol.14
, pp. 2128-2135
-
-
Rual, J.F.1
-
23
-
-
0032703169
-
A genetic strategy to eliminate self-activator baits prior to high-throughput yeast two-hybrid screens
-
23 Walhout, A.J., Vidal, M., A genetic strategy to eliminate self-activator baits prior to high-throughput yeast two-hybrid screens. Genome res. 9 (1999), 1128–1134.
-
(1999)
Genome res.
, vol.9
, pp. 1128-1134
-
-
Walhout, A.J.1
Vidal, M.2
-
24
-
-
84874232489
-
The coming age of complete, accurate, and ubiquitous proteomes
-
24 Mann, M., et al. The coming age of complete, accurate, and ubiquitous proteomes. Mol. cell 49 (2013), 583–590.
-
(2013)
Mol. cell
, vol.49
, pp. 583-590
-
-
Mann, M.1
-
25
-
-
77957221582
-
A survey of computational methods and error rate estimation procedures for peptide and protein identification in shotgun proteomics
-
25 Nesvizhskii, A.I., A survey of computational methods and error rate estimation procedures for peptide and protein identification in shotgun proteomics. J. of proteomics 73 (2010), 2092–2123.
-
(2010)
J. of proteomics
, vol.73
, pp. 2092-2123
-
-
Nesvizhskii, A.I.1
-
26
-
-
84862660561
-
Computational and informatics strategies for identification of specific protein interaction partners in affinity purification mass spectrometry experiments
-
26 Nesvizhskii, A.I., Computational and informatics strategies for identification of specific protein interaction partners in affinity purification mass spectrometry experiments. Proteomics 12 (2012), 1639–1655.
-
(2012)
Proteomics
, vol.12
, pp. 1639-1655
-
-
Nesvizhskii, A.I.1
-
27
-
-
84874625369
-
Proteoform: a single term describing protein complexity
-
27 Smith, L.M., et al. Proteoform: a single term describing protein complexity. Nat. methods 10 (2013), 186–187.
-
(2013)
Nat. methods
, vol.10
, pp. 186-187
-
-
Smith, L.M.1
-
28
-
-
48649096489
-
A protein domain-based interactome network for C. elegans early embryogenesis
-
28 Boxem, M., et al. A protein domain-based interactome network for C. elegans early embryogenesis. Cell 134 (2008), 534–545.
-
(2008)
Cell
, vol.134
, pp. 534-545
-
-
Boxem, M.1
-
29
-
-
84859208501
-
Protein interaction data curation: the International Molecular Exchange (IMEx) consortium
-
29 Orchard, S., et al. Protein interaction data curation: the International Molecular Exchange (IMEx) consortium. Nat. methods 9 (2012), 345–350.
-
(2012)
Nat. methods
, vol.9
, pp. 345-350
-
-
Orchard, S.1
-
30
-
-
58149242456
-
An experimentally derived confidence score for binary protein–protein interactions
-
30 Braun, P., et al. An experimentally derived confidence score for binary protein–protein interactions. Nat. methods 6 (2009), 91–97.
-
(2009)
Nat. methods
, vol.6
, pp. 91-97
-
-
Braun, P.1
-
31
-
-
77956321519
-
Exhaustive benchmarking of the yeast two-hybrid system
-
author reply 668
-
31 Chen, Y.C., et al. Exhaustive benchmarking of the yeast two-hybrid system. Nat. methods 7 (2010), 667–668 author reply 668.
-
(2010)
Nat. methods
, vol.7
, pp. 667-668
-
-
Chen, Y.C.1
-
32
-
-
84872379791
-
A comparison and optimization of yeast two-hybrid systems
-
32 Caufield, J.H., et al. A comparison and optimization of yeast two-hybrid systems. Methods 58 (2012), 317–324.
-
(2012)
Methods
, vol.58
, pp. 317-324
-
-
Caufield, J.H.1
-
33
-
-
58149213932
-
Literature-curated protein interaction datasets
-
33 Cusick, M.E., et al. Literature-curated protein interaction datasets. Nat. methods 6 (2009), 39–46.
-
(2009)
Nat. methods
, vol.6
, pp. 39-46
-
-
Cusick, M.E.1
-
35
-
-
33847744247
-
How complete are current yeast and human protein-interaction networks?
-
35 Hart, G.T., et al. How complete are current yeast and human protein-interaction networks?. Genome biol., 7, 2006, 120.
-
(2006)
Genome biol.
, vol.7
, pp. 120
-
-
Hart, G.T.1
-
36
-
-
84889560325
-
Extracting insight from noisy cellular networks
-
36 Landry, C.R., et al. Extracting insight from noisy cellular networks. Cell 155 (2013), 983–989.
-
(2013)
Cell
, vol.155
, pp. 983-989
-
-
Landry, C.R.1
-
37
-
-
0036580169
-
Protein interactions: two methods for assessment of the reliability of high throughput observations
-
37 Deane, C.M., et al. Protein interactions: two methods for assessment of the reliability of high throughput observations. Mol. cell. proteomics 1 (2002), 349–356.
-
(2002)
Mol. cell. proteomics
, vol.1
, pp. 349-356
-
-
Deane, C.M.1
-
38
-
-
65349149138
-
How perfect can protein interactomes be?
-
38 Levy, E.D., et al. How perfect can protein interactomes be?. Sci. signaling, 2, 2009, pe11.
-
(2009)
Sci. signaling
, vol.2
, pp. pe11
-
-
Levy, E.D.1
-
39
-
-
0037432528
-
How reliable are experimental protein–protein interaction data?
-
39 Sprinzak, E., et al. How reliable are experimental protein–protein interaction data?. J. Mol. Biol. 327 (2003), 919–923.
-
(2003)
J. Mol. Biol.
, vol.327
, pp. 919-923
-
-
Sprinzak, E.1
-
40
-
-
0346555269
-
Optimization of specificity in a cellular protein interaction network by negative selection
-
40 Zarrinpar, A., et al. Optimization of specificity in a cellular protein interaction network by negative selection. Nature 426 (2003), 676–680.
-
(2003)
Nature
, vol.426
, pp. 676-680
-
-
Zarrinpar, A.1
-
41
-
-
84964490303
-
An inter-species protein–protein interaction network across vast evolutionary distance
-
41 Zhong, Q., et al. An inter-species protein–protein interaction network across vast evolutionary distance. Mol. syst. biol., 12, 2016, 865.
-
(2016)
Mol. syst. biol.
, vol.12
, pp. 865
-
-
Zhong, Q.1
-
42
-
-
0034069495
-
Gene ontology: tool for the unification of biology. The Gene Ontology Consortium
-
42 Ashburner, M., et al. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat. genet. 25 (2000), 25–29.
-
(2000)
Nat. genet.
, vol.25
, pp. 25-29
-
-
Ashburner, M.1
-
43
-
-
44349113144
-
Estimating the size of the human interactome
-
43 Stumpf, M.P., et al. Estimating the size of the human interactome. Proc. Natl. Acad. Sci. U.S.A. 105 (2008), 6959–6964.
-
(2008)
Proc. Natl. Acad. Sci. U.S.A.
, vol.105
, pp. 6959-6964
-
-
Stumpf, M.P.1
-
44
-
-
84904469894
-
A million peptide motifs for the molecular biologist
-
44 Tompa, P., et al. A million peptide motifs for the molecular biologist. Mol. cell 55 (2014), 161–169.
-
(2014)
Mol. cell
, vol.55
, pp. 161-169
-
-
Tompa, P.1
-
45
-
-
84949099771
-
A strategy for dissecting the architectures of native macromolecular assemblies
-
45 Shi, Y., et al. A strategy for dissecting the architectures of native macromolecular assemblies. Nat. methods 12 (2015), 1135–1138.
-
(2015)
Nat. methods
, vol.12
, pp. 1135-1138
-
-
Shi, Y.1
-
46
-
-
84962576477
-
Cross-linking immunoprecipitation-MS (xIP-MS): topological analysis of chromatin-associated protein complexes using single affinity purification
-
46 Makowski, M.M., et al. Cross-linking immunoprecipitation-MS (xIP-MS): topological analysis of chromatin-associated protein complexes using single affinity purification. Mol. cell. proteomics 15 (2016), 854–865.
-
(2016)
Mol. cell. proteomics
, vol.15
, pp. 854-865
-
-
Makowski, M.M.1
-
47
-
-
84949106630
-
Proteome-wide profiling of protein assemblies by cross-linking mass spectrometry
-
47 Liu, F., et al. Proteome-wide profiling of protein assemblies by cross-linking mass spectrometry. Nat. methods 12 (2015), 1179–1184.
-
(2015)
Nat. methods
, vol.12
, pp. 1179-1184
-
-
Liu, F.1
-
48
-
-
84951304664
-
F508 CFTR interactome remodelling promotes rescue of cystic fibrosis
-
48 Pankow, S., et al. F508 CFTR interactome remodelling promotes rescue of cystic fibrosis. Nature 528 (2015), 510–516.
-
(2015)
Nature
, vol.528
, pp. 510-516
-
-
Pankow, S.1
-
49
-
-
84863003268
-
Tissue-specific alternative splicing remodels protein–protein interaction networks
-
49 Ellis, J.D., et al. Tissue-specific alternative splicing remodels protein–protein interaction networks. Mol. Cell. 46 (2012), 884–892.
-
(2012)
Mol. Cell.
, vol.46
, pp. 884-892
-
-
Ellis, J.D.1
-
50
-
-
84879143595
-
Alternative splicing of intrinsically disordered regions and rewiring of protein interactions
-
50 Buljan, M., et al. Alternative splicing of intrinsically disordered regions and rewiring of protein interactions. Curr. Opin. Struc. Biol. 23 (2013), 443–450.
-
(2013)
Curr. Opin. Struc. Biol.
, vol.23
, pp. 443-450
-
-
Buljan, M.1
-
51
-
-
84958182784
-
Widespread expansion of protein interaction capabilities by alternative splicing
-
51 Yang, X.P., et al. Widespread expansion of protein interaction capabilities by alternative splicing. Cell 164 (2016), 805–817.
-
(2016)
Cell
, vol.164
, pp. 805-817
-
-
Yang, X.P.1
-
52
-
-
84928389942
-
Widespread macromolecular interaction perturbations in human genetic disorders
-
52 Sahni, N., et al. Widespread macromolecular interaction perturbations in human genetic disorders. Cell 161 (2015), 647–660.
-
(2015)
Cell
, vol.161
, pp. 647-660
-
-
Sahni, N.1
-
53
-
-
84925867326
-
Phospho-tyrosine dependent protein–protein interaction network
-
53 Grossmann, A., et al. Phospho-tyrosine dependent protein–protein interaction network. Mol. syst. biol., 11, 2015, 794.
-
(2015)
Mol. syst. biol.
, vol.11
, pp. 794
-
-
Grossmann, A.1
-
54
-
-
84890661376
-
Studying post-translational modifications with protein interaction networks
-
54 Woodsmith, J., Stelzl, U., Studying post-translational modifications with protein interaction networks. Curr. Opin. Struc. Biol 24 (2014), 34–44.
-
(2014)
Curr. Opin. Struc. Biol
, vol.24
, pp. 34-44
-
-
Woodsmith, J.1
Stelzl, U.2
-
55
-
-
84962217539
-
Survey of variation in human transcription factors reveals prevalent DNA binding changes
-
55 Barrera, L.A., et al. Survey of variation in human transcription factors reveals prevalent DNA binding changes. Science 351 (2016), 1450–1454.
-
(2016)
Science
, vol.351
, pp. 1450-1454
-
-
Barrera, L.A.1
-
56
-
-
84928395759
-
Human gene-centered transcription factor networks for enhancers and disease variants
-
56 Fuxman Bass, J.I., Human gene-centered transcription factor networks for enhancers and disease variants. Cell 161 (2015), 661–673.
-
(2015)
Cell
, vol.161
, pp. 661-673
-
-
Fuxman Bass, J.I.1
-
57
-
-
25144498379
-
A human protein–protein interaction network: a resource for annotating the proteome
-
57 Stelzl, U., et al. A human protein–protein interaction network: a resource for annotating the proteome. Cell 122 (2005), 957–968.
-
(2005)
Cell
, vol.122
, pp. 957-968
-
-
Stelzl, U.1
-
58
-
-
27144530248
-
Towards a proteome-scale map of the human protein–protein interaction network
-
58 Rual, J.F., et al. Towards a proteome-scale map of the human protein–protein interaction network. Nature 437 (2005), 1173–1178.
-
(2005)
Nature
, vol.437
, pp. 1173-1178
-
-
Rual, J.F.1
-
59
-
-
33947219266
-
Large-scale mapping of human protein–protein interactions by mass spectrometry
-
59 Ewing, R.M., et al. Large-scale mapping of human protein–protein interactions by mass spectrometry. Mol. syst. biol., 3, 2007, 89.
-
(2007)
Mol. syst. biol.
, vol.3
, pp. 89
-
-
Ewing, R.M.1
-
60
-
-
84866134921
-
A high-throughput approach for measuring temporal changes in the interactome
-
60 Kristensen, A.R., et al. A high-throughput approach for measuring temporal changes in the interactome. Nat. methods 9 (2012), 907–909.
-
(2012)
Nat. methods
, vol.9
, pp. 907-909
-
-
Kristensen, A.R.1
-
61
-
-
79959898376
-
Prioritizing candidate disease genes by network-based boosting of genome-wide association data
-
61 Lee, I., et al. Prioritizing candidate disease genes by network-based boosting of genome-wide association data. Genome res. 21 (2011), 1109–1121.
-
(2011)
Genome res.
, vol.21
, pp. 1109-1121
-
-
Lee, I.1
-
62
-
-
75549091794
-
CORUM: the comprehensive resource of mammalian protein complexes – 2009
-
62 Ruepp, A., et al. CORUM: the comprehensive resource of mammalian protein complexes – 2009. Nucleic acids res. 38 (2010), D497–501.
-
(2010)
Nucleic acids res.
, vol.38
, pp. D497-501
-
-
Ruepp, A.1
-
63
-
-
84941051170
-
STRING v10: protein–protein interaction networks, integrated over the tree of life
-
63 Szklarczyk, D., et al. STRING v10: protein–protein interaction networks, integrated over the tree of life. Nucleic acids res. 43 (2015), D447–D452.
-
(2015)
Nucleic acids res.
, vol.43
, pp. D447-D452
-
-
Szklarczyk, D.1
-
64
-
-
77954269901
-
The GeneMANIA prediction server: biological network integration for gene prioritization and predicting gene function
-
64 Warde-Farley, D., et al. The GeneMANIA prediction server: biological network integration for gene prioritization and predicting gene function. Nucleic acids res. 38 (2010), W214–220.
-
(2010)
Nucleic acids res.
, vol.38
, pp. W214-220
-
-
Warde-Farley, D.1
-
65
-
-
44449102838
-
Next-generation high-density self-assembling functional protein arrays
-
65 Ramachandran, N., et al. Next-generation high-density self-assembling functional protein arrays. Nat. methods 5 (2008), 535–538.
-
(2008)
Nat. methods
, vol.5
, pp. 535-538
-
-
Ramachandran, N.1
|